@echo off
zenity --file-selection --title="Select first fasta input" > tmp
set /p input1= < tmp
del tmp
echo Selected %input1%
zenity zenity --entry --text "Output file for the first alignment" > tmp
set /p output1= < tmp
del tmp
zenity zenity --entry --text "Enter the prefix of the first fasta file (optional)" > tmp
set /p prefix1= < tmp
del tmp
zenity --file-selection --title="Select second fasta input" > tmp
set /p input2= < tmp
del tmp
echo Selected %input2%
zenity zenity --entry --text "Output file for the second alignment" > tmp
set /p output2= < tmp
del tmp
zenity zenity --entry --text "Enter the prefix of the second fasta file (optional)" > tmp
set /p prefix2= < tmp
del tmp
intalign.exe --input1 "%input1%"  --input2 "%input2%" --output1 %output1% --output2 %output2% --prefix1 %prefix1% --prefix2 %prefix2%
pause


